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BioC experimental data: BUILD report for RforProteomics on moscato1

This page was generated on 2016-09-21 21:57:13 -0700 (Wed, 21 Sep 2016).

Package 235/304HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.11.2
Laurent Gatto
Snapshot Date: 2016-09-21 09:20:16 -0700 (Wed, 21 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics
Last Changed Rev: 3773 / Revision: 3889
Last Changed Date: 2016-05-15 13:21:08 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: RforProteomics
Version: 1.11.2
Command: chmod a+r RforProteomics -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2016-09-21 11:08:32 -0700 (Wed, 21 Sep 2016)
EndedAt: 2016-09-21 11:26:21 -0700 (Wed, 21 Sep 2016)
EllapsedTime: 1069.4 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   chmod a+r RforProteomics -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RforProteomics
###
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* checking for file 'RforProteomics/DESCRIPTION' ... OK
* preparing 'RforProteomics':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval,
    evalq, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max,
    which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.99.1 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws


This is the 'RforProteomics' version 1.11.2.

  To get started, visit
    http://lgatto.github.com/RforProteomics/

  or, in R, open package vignettes by typing
    RforProteomics() # R/Bioc for proteomics overview
    RProtVis()       # R/Bioc for proteomics visualisation

  For a full list of available documents:
    vignette(package='RforProteomics')


Bioconductor version 3.4 (BiocInstaller 1.23.9), ?biocLite for help

Attaching package: 'xtable'

The following object is masked from 'package:RforProteomics':

    display


This is MALDIquant version 1.15
Quantitative Analysis of Mass Spectrometry Data
 See '?MALDIquant' for more information about this package.


Attaching package: 'MALDIquant'

The following objects are masked from 'package:MSnbase':

    estimateNoise, intensity, isEmpty, mz

The following objects are masked from 'package:ProtGenerics':

    intensity, mass, mz, mz<-

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:MALDIquant':

    isEmpty

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:MALDIquant':

    trim

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.13.15 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.


This is pRolocdata version 1.11.8.
Use 'pRolocdata()' to list available data sets.
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Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
Quitting from lines 159-189 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
object 'tmp' not found
Execution halted